Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles
Sissy Bassani 1 2, Jacqueline Chrast 1, Giovanna Ambrosini 3 4, Norine Voisin 1 5, Frédéric Schütz 6, Alfredo Brusco 7 8, Fabio Sirchia 7 8 9 10, Lydia Turban 11, Susanna Schubert 11, Rami Abou Jamra 11, Jan-Ulrich Schlump 12, Desiree DeMille 13, Pinar Bayrak-Toydemir 14, Gary Rex Nelson 14, Kristen Nicole Wong 14, Laura Duncan 15 16, Mackenzie Mosera 15, Christian Gilissen 17, Lisenka E L M Vissers 17, Rolph Pfundt 17, Rogier Kersseboom 18, Hilde Yttervik 19, Geir Åsmund Myge Hansen 19, Marie Falkenberg Smeland 20, Kameryn M Butler 21, Michael J Lyons 21, Claudia M B Carvalho 22 23, Chaofan Zhang 23, James R Lupski 23 24 25 26, Lorraine Potocki 23 26, Leticia Flores-Gallegos 27, Rodrigo Morales-Toquero 27, Florence Petit 28, Binnaz Yalcin 29, Annabelle Tuttle 30, Houda Zghal Elloumi 30, Lane McCormick 31, Mary Kukolich 31, Oliver Klaas 32, Judit Horvath 32, Marcello Scala 33 34, Michele Iacomino 34, Francesca Operto 35, Federico Zara 33 34, Karin Writzl 36 37, Aleš Maver 36, Maria K Haanpää 38, Pia Pohjola 38, Harri Arikka 39, Anneke J A Kievit 40, Camilla Calandrini 40, Christian Iseli 3 4, Nicolas Guex 3 4, Alexandre Reymond 41
Affiliations expand
- . 2024 May 30;16(1):72.
- doi: 10.1186/s13073-024-01339-y.
- PMID: 38811945
- PMCID: PMC11137988
- DOI: 10.1186/s13073-024-01339-y
Abstract
Background: We previously described the KINSSHIP syndrome, an autosomal dominant disorder associated with intellectual disability (ID), mesomelic dysplasia and horseshoe kidney, caused by de novo variants in the degron of AFF3. Mouse knock-ins and overexpression in zebrafish provided evidence for a dominant-negative mode of action, wherein an increased level of AFF3 resulted in pathological effects.
Methods: Evolutionary constraints suggest that other modes-of-inheritance could be at play. We challenged this hypothesis by screening ID cohorts for individuals with predicted-to-be damaging variants in AFF3. We used both animal and cellular models to assess the deleteriousness of the identified variants.
Results: We identified an individual with a KINSSHIP-like phenotype carrying a de novo partial duplication of AFF3 further strengthening the hypothesis that an increased level of AFF3 is pathological. We also detected seventeen individuals displaying a milder syndrome with either heterozygous Loss-of-Function (LoF) or biallelic missense variants in AFF3. Consistent with semi-dominance, we discovered three patients with homozygous LoF and one compound heterozygote for a LoF and a missense variant, who presented more severe phenotypes than their heterozygous parents. Matching zebrafish knockdowns exhibit neurological defects that could be rescued by expressing human AFF3 mRNA, confirming their association with the ablation of aff3. Conversely, some of the human AFF3 mRNAs carrying missense variants identified in affected individuals did not rescue these phenotypes. Overexpression of mutated AFF3 mRNAs in zebrafish embryos produced a significant increase of abnormal larvae compared to wild-type overexpression further demonstrating deleteriousness. To further assess the effect of AFF3 variation, we profiled the transcriptome of fibroblasts from affected individuals and engineered isogenic cells harboring + / + , KINSSHIP/KINSSHIP, LoF/ + , LoF/LoF or KINSSHIP/LoF AFF3 genotypes. The expression of more than a third of the AFF3 bound loci is modified in either the KINSSHIP/KINSSHIP or the LoF/LoF lines. While the same pathways are affected, only about one third of the differentially expressed genes are common to the homozygote datasets, indicating that AFF3 LoF and KINSSHIP variants largely modulate transcriptomes differently, e.g. the DNA repair pathway displayed opposite modulation.
Conclusions: Our results and the high pleiotropy shown by variation at this locus suggest that minute changes in AFF3 function are deleterious.